Association with a sea anemone alters the skin microbiome of clownfish

Abstract

Host-associated microbes play important roles in animal health. Clownfish and anemones form a mutualistic relationship where external surfaces are in constant contact with one another. The effects of this mutualism on the skin mucosal microbiome of clownfish are unknown. We monitored the mucosal microbiome of the clownfish Amphiprion clarkii before, during and after association (hosting) with the anemone Entacmaea quadricolor. Microbiome composition differed significantly between hosting and non-hosting clownfish. Upon separation of clownfish from anemones, the microbiome of post-hosting fish converged to resemble that of non-hosting fish. Bacterial sequence variants that significantly distinguished hosting from non-hosting clownfish were more abundant in the anemone microbiome and that of hosting fish, compared to non-hosting fish, suggesting transfer from or enrichment by the anemone. These results show that direct contact mutualism results in significant but reversible microbiome shifts, raising questions about a potential microbial role in mediating the fish–anemone interaction.

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Acknowledgements

This work was supported by Simons Foundation (award 346253 of FJS) and the Teasley Endowment to the Georgia Institute of Technology. We are grateful to the Physiological Research Laboratory staff at the Georgia Institute of Technology for the dedicated care of the research animals, and to Sustainable Aquatics for supplying animals. Research was conducted under IACUC permit A100024. ZAP, FJS, NVP and DJP developed the experimental design. ZAP, NVP, MEM and AMC performed the experimental procedures. ZAP, NVP and FJS contributed to data analysis, and ZAP and FJS wrote the manuscript with editorial assistance from all authors.